The presentation provides a brief discussion about mechanism of submergence tolerance in rice crop. The success story of introgression of sub 1 in rice crop.

1. Sub1 GENE
Submitted by
Ananda Lekshmi L
ID NO. 2020608005
GPB 607 ADVANCES IN CROP
BREEDING (3+0)
A TRIUMPH OF MAB

2.  Rice cultivation and flooding are considered synonymous
 Rice is the only crop plant adapted to aquatic - well-developed
aerenchyma tissues that facilitate oxygen diffusion through continuous
air spaces from shoot to root - avoid anoxia development in roots
 The floods bring water and nutrients to the rice plants, but can also kill
the plants if too deep or prolonged
 Complete submergence due to frequent flooding can adversely affect
plant growth and yield
INTRODUCTION:

3. Three major types of flooding mechanisms in rice plants:
(1) short-duration flooding of less than 3 weeks, referred to as
submergence – flash flood;
(2) long-duration flooding, sometimes referred to as stagnant
flooding;
(3) flooding during germination, referred to as anaerobic
germination;
Flooding from rainwater usually results in clear water and causes
less crop damage than that with silted or turbid water.
Types of flooding

4.  In shallow, irrigated rice (a), water
depth usually remains well below 25
cm for the crop duration.
 In medium-deep conditions (b),
water depths can remain between 25
and 50 cm for prolonged periods,
 In deep water and floating rice (c),
water depths can go to 1 m or more
for an appreciable period of the
season.
 Submergence is a short-term stress of
2–3 weeks and can occur in shallow
flooded (d) or stagnant flooded (e)
conditions
Flooding patterns in rice:

6.  Plants are submerged for up to a few weeks - survive upto 15 days
 Two famous pure-line selections FR13A and FR43B - farmers’ traditional
landraces Dhalputtia and Bhetnasia, respectively - isolated at the Cuttack
station, Odisha
 FR13A was known to CRRI even in 1950 as a submergence-tolerant cultivar
 FR13A occupied the core position in the National and International rice
breeding programmes from which the submergence tolerance gene SUB1A was
identified and cloned
 highly tolerant FR13A (and its progeny) controlled by the SUB1 QTL on
chromosome 9 (Xu and Mackill 1996)
 The SUB1A gene has been found in wild rice progenitor Oryza rufipogon (Li et
al. 2011)
 SUB1A gene of O. nivara is on chromosome 1
SHORT TERM FLOOD ;
SUBMERGENCE

7.  Quiescence and elongation (expansion) - opposite strategies – depends
upon the nature of flooding
 The ethylene response factor genes Snorkel1 (SK1) and Snorkel2
(SK2) allow rice to adapt to deep water
 Submergence1 A-1 (SUB1A-1) allows rice to acclimatize under flash
flooding (Xu et al., 2006; Hattori et al., 2009; Nagai et al., 2010)
 The QTL on chromosome 12 was the most effective for deepwater
response (Nemoto et al., 2004; Hattori et al., 2007, 2008)
 the QTL on chromosome 9 was most important for flash flood
response (Xu and Mackill, 1996)
 Both SKs genes and SUB1A encode ethylene-responsive factor -
transcription factor - connected to gibberellin biosynthesis or signal
transduction
Genes related to escape and
quiescence strategies

8.  In the SUB1 region, three similar genes encode the AP2/ERF
domain: SUB1A, SUB1B and SUB1C located tandemly on
chromosome 9 in FR13A
 Submergence-intolerant varieties possess SUB1B and
SUB1C, but lack SUB1A
 Introduction of SUB1A into submergence-intolerant varieties
confers submergence tolerance (Fukao et al., 2006; Xu et al.,
2006; Neeraja et al., 2007; Septiningsih et al., 2009)
 SUB1A negatively regulates the transcription of GA
biosynthesis, to reduce energy consumption during
submergence.

9. Slender rice-1 (SLR1) and SLR1 Like-1 (SLRL1)
are repressors of GA signaling
The amount of SLR1 protein is elevated after
submergence in submergence-tolerant rice but not in
submergence-intolerant rice
SK1 and SK2 are upregulated by the submergence-
induced accumulation of ethylene in internodes,
consistent with the essential role of ethylene in GA-
stimulated underwater shoot elongation (Jackson,
2008).

11.  There exist linkage of submergence
tolerance with the undesirable traits
of the donor FR13A
 The discovery and fine-mapping of
the SUB1 QTL, which largely
contributes to submergence tolerance
of FR13A
 Closely linked and gene-based
markers were developed to perform
marker-assisted backcrossing
(MABC) to convert susceptible mega
varieties into tolerant lines without
significantly altering beneficial traits
of those superior varieties
(Septiningsih et al. 2013a).
Breeding for submergence
tolerance:

12.  IRRI successfully converted six mega varieties using two
improved lines derived from FR13A as donors for
submergence tolerance using the following mega varieties as
recurrent parents:
 IR64 (Philippines);
 Swarna,
 Samba Mahsuri, and
 CR1009 or Savitri (India);
 BR11 (Bangladesh); and
 Tadokham 1 (TDK1; Laos)

13. Popular variety CO 43 exhibited susceptibility against submergence.
Tolerant FR13A used as donor
Introgression of Sub1 locus from FR13A into CO 43 was confirmed by screening the
F2:3 progenies harbouring CO 43 and FR13A alleles of Sub1 locus linked markers
against submergence
Quick regeneration following submergence is a desirable trait under prolonged
flooding, as it can ensure early recovery and production of sufficient biomass for
optimum productivity

14. Background selection enabled identification of progenies possessing 65.40% of
recurrent parent genome at BC1F1, 83.33% of recurrent parent genome at BC2F1 and
95.78% of recurrent parent genome at BC3F3 generation

15.  CO 43 NILs exhibited a significantly higher level of survival rate
upon submergence when compared to CO 43
 This demonstrated that Sub 1 confers tolerance to submergence in
different genetic backgrounds as already demonstrated in various
other genetic backgrounds like Swarna, Samba Mahsuri, TDK Sub 1,
BR 11 Sub 1, CR 1009 Sub1 etc. (Neeraja et al. 2007; Septiningsih et
al. 2009)
 Field evaluation of improved NILs along with recurrent parent and
Swarna Sub1 (positive check) across several locations at a national
level indicated that the NILs were similar to CO 43 in all agronomic
values under normal conditions
 NILs exhibited 20−25% yield advantage over its recurrent parent
CO 43 under submergence which clearly indicated that this
improved version can be cultivated in places wherever this mega
variety is cultivated (AICRIP 2015, 2016).

16. Introgression of SUB1 QTL -has no deleterious effects on yield
and yield attributes
 There was not much variation in the yields of recurrent parent
and Sub1 introgressed lines under favourable conditions
Parent materials should be carefully selected before
introgression of SUB1
Cultivars with greater initial vigour are considered better
Introgression of SUB1 in a rice cultivar increases its
submergence tolerance but the tolerance level is not greater
than FR13A
Look for new genes/QTLs for realizing greater submergence
tolerance
Inference about SUB1

17. Target traits for submergence breeding
Vegetative vigor
High tillering
ability
Erect leaves
Longer, wide and
thick leaves
Grain
dormancy
Plant height
Lodging
resistance
High fertility

18.  Rice Genomics, Genetics and Breeding; Takuji Sasaki • Motoyuki
Ashikari
 Sarkar RK, Das KK, Panda D, Reddy JN, Patnaik SSC, Patra BC and Singh
DP 2014. Submergence tolerance in rice: Biophysical Constraints,
Physiological basis and Identification of Donors. Central Rice Research
Institute, Cuttck, India. p.36
 Development and Rapid Adoption of Submergence-Tolerant (Sub1)
Rice Varieties D. J. Mackill,*,† A. M. Ismail,* U. S. Singh,‡ R. V.
Labios,§ andT. R. Paris*
 Rahman, Hifzur, Vijayalakshmi Dakshinamurthi, Sasikala Ramasamy,
Sudha Manickam, Ashok Kumar Kaliyaperumal, Suchismita Raha, Naresh
Panneerselvam et al. "Introgression of submergence tolerance into CO
43, a popular rice variety of India, through marker-assisted backcross
breeding." Czech Journal of Genetics and Plant Breeding 54, no. 3 (2018):
101-108.
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